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Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in early UV response

ABSTRACT: Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in early UV response

PROVIDER: PRJNA439217 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6869150_1.fastq.gz	Fastqsanger.gz
	SRR6869150_2.fastq.gz	Fastqsanger.gz
	SRR6869160_1.fastq.gz	Fastqsanger.gz
	SRR6869160_2.fastq.gz	Fastqsanger.gz
	SRR6869170_1.fastq.gz	Fastqsanger.gz

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Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in early UV response

Project description:Extremophilic archaea like all organisms experience potentially life-threatening conditions including UV light, which induces severe DNA damage. Since the alternative general transcription factor (GTF) TFB3 has been proposed to play a key role in UV stress response in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius, we investigated the expression of TFB3 on protein level including in vivo protein-protein interaction studies, tfb3 reporter gene assays and creation of a tfb3 insertion mutant to study early differential gene expression upon UV treatment (after 45 and 90 minutes). Our results allowed differentiating between the TFB3-dependent and TFB3-independent early UV response in S. acidocaldarius. The early TFB3-independent UV response includes the repression of nucleotide biosynthesis and transport, replication and cell cycle progression in order to allow DNA repair. The TFB3-dependent UV response is characterized by the early induction of TFB3, which is a prerequisite for the following TFB3-dependent expression of genes involved in ups pili formation and the Ced DNA importer. Both structures facilitate the transfer of DNA to allow repair via homologous recombination. The fact, that all genes are downregulated in the tfb3 mutant compared to the reference strain, confirms the hypothesis that TFB3 acts as an activator of transcription.

2020-03-20 | GSE112071 | GEO

Transcription profiling of hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius to UV irradiation

Project description:Analysis of transcriptional response to UV irradiation in two related crenarchaea, Sulfolobus solfataricus and Sulfolobus acidocaldarius.

2007-11-21 | E-MEXP-1252 | biostudies-arrayexpress

Genome-wide interaction map of YtrA transcription factor in S. Acidocaldarius

Project description:We report the characterization of GntR-like regulator in the Archaeon Sulfolobus acidocaldarius by looking at the genome wide interaction map of the protein in vivo

2019-09-26 | GSE129461 | GEO

Transcriptome analysis of Sulfolobus acidocaldarius DSM 639 under sugar-free and sugar-rich conditions

Project description:Sulfolobus acidocaldarius is an obligate aerobe that grows in hot and acidic environments. S. acidocaldarius have been reported to grow on a variety of organic compounds as carbon and energy sources. However, little is known about systemic elucidation of carbon utilization for biomass formation and energy metabolism in S. acidocaldarius. In this analysis, the effect of glucose on genome-wide transcriptional profiling in S. acidocaldarius DSM 639 was investigated by RNA-Seq technology.

2020-11-15 | GSE107083 | GEO

Sulfolobus acidocaldarius phosphoproteome

Project description:Shotgun phosphoproteome of Sulfolobus acidocaldarius using PAciFIC technique. Briefly, proteins were denatured, alkylated, trypsine digestion, SCX separation Fractionated peptides were analysed on Bruker HCTultra. Data processing and bioinformatics: data from mass spectrometry were then extracted to mgf format using Bruker Data Analysis V4.0 with a MRM script, these were then were searched against the Sulfolobus acidocaldarius database (containing 2223 proteins) downloaded from NCBI in March 2010 using Phenyx V 2.6 (Genebio, Geneva). The searches were performed using parameters as follows: carbamidomethylation of cysteine (fixed modification), oxidation of methionine (variation), and phosphorylation of serine, tyrosine, threonine (variation), trypsin with 2 missed cleavages. Furthermore, other parameters such as parent, MS/MS, tolerances were set at 2.0 and 0.8 Da, respectively, whilst minimum peptide length, z-score, p-value and AC score were set at 5, 5.5, 10-5, and 5.5 respectively.

2014-04-15 | PXD000289 | Pride

Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response.

Project description:Exposure to UV light can result in severe DNA damage. The alternative general transcription factor (GTF) TFB3 has been proposed to play a key role in the UV stress response in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. Reporter gene assays confirmed that tfb3 is upregulated 90-180 min after UV treatment. In vivo tagging and immunodetection of TFB3 confirmed the induced expression at 90 min. Analysis of a tfb3 insertion mutant showed that genes encoding proteins of the Ups pili and the Ced DNA importer are no longer induced in a tfb3 insertion mutant after UV treatment, which was confirmed by aggregation assays. Thus, TFB3 plays a crucial role in the activation of these genes. Genome wide transcriptome analysis allowed a differentiation between a TFB3-dependent and a TFB3-independent early UV response. The TFB3-dependent UV response is characterized by the early induction of TFB3, followed by TFB3-dependent expression of genes involved in e.g. Ups pili formation and the Ced DNA importer. Many genes were downregulated in the tfb3 insertion mutant confirming the hypothesis that TFB3 acts as an activator of transcription. The TFB3-independent UV response includes the repression of nucleotide metabolism, replication and cell cycle progression in order to allow DNA repair.

| S-EPMC6101591 | biostudies-literature

The genome-scale DNA-binding of FadR transcription factor in Sulfolobus acidocaldarius

Project description:This is ChIPseq result of FadR (Saci_1107), which is the only TetR family regulator presented in Sulfolobus acidocaldarius. The aim of the study is to gain insights into the function of TetR regulator by analyzing its whole genome binding sites.

2017-12-14 | GSE108039 | GEO

The genome-scale DNA-binding of FadR transcription factor in Sulfolobus acidocaldarius

Project description:This is ChIPseq result of FadR, which is the only TetR family regulator presented in Sulfolobus acidocaldarius. The aim of the study is to gain insights into the function of TetR regulator by analyzing its whole genome binding sites.

2017-12-30 | E-MTAB-6328 | biostudies-arrayexpress

Transcriptome of S. acidocaldarius MW001 strain grown as biofilm or planktonic cells and transcriptomic profile of an RNaseR-treated S. acidocaldarius MW001 small RNA sample

Project description:Total RNAs were isolated from the thermophilic archaeon Sulfolobus acidocaldarius MW001 and subjected to Illumina sequencing. A differential gene expression analysis was performed to identify ncRNA in biofilm- associated cells and planktonically grown cells. Additionally, the small RNA subpopulation of the transcriptome was subjected to RNaseR digestion prior to Illumina sequencing. An abundant double-stranded RNA was identified.

2017-05-31 | GSE99484 | GEO

Sulfolobus acidocaldarius

Project description:Sulfolobus acidocaldarius Raw sequence reads

| PRJNA1121029 | ENA